LXL04_022697 | RubberDandelionOmics

Gene overview

LXL04_022697

Reference: OH-1004 Chr: Chr05 Coordinates: 5220461-5224007 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2169 bp · LXL04_022697|LXL04_022697|OH1004|cDNA

ATGGTCGGCGGTGGAGGCGATGCTCCGCCACCACCTCCTATAAACGGCGGCGAGTTCCTTCTACACTTGCTCAAAAATCCACCACAGCATCCTCGTTCGCACTCCCAACCACCACCGCCACAACCGTCACAAGTACTCCCTCACGATCCCGCCGTCGCTGCTGTTGGCCCCTCGATGCCTTTCCCGCCACAGTCATTCCCATCACATGGTACCGATTACCTCCTCCCCTCCCGCCCTCCGCTTTTCCCACCTCATAATTA...

CDS

Download CDS FASTA

2169 bp · LXL04_022697|LXL04_022697|OH1004|CDS

ATGGTCGGCGGTGGAGGCGATGCTCCGCCACCACCTCCTATAAACGGCGGCGAGTTCCTTCTACACTTGCTCAAAAATCCACCACAGCATCCTCGTTCGCACTCCCAACCACCACCGCCACAACCGTCACAAGTACTCCCTCACGATCCCGCCGTCGCTGCTGTTGGCCCCTCGATGCCTTTCCCGCCACAGTCATTCCCATCACATGGTACCGATTACCTCCTCCCCTCCCGCCCTCCGCTTTTCCCACCTCATAATTA...

Protein

Download Protein FASTA

722 aa · LXL04_022697|LXL04_022697|OH1004|PROTEIN

MVGGGGDAPPPPPINGGEFLLHLLKNPPQHPRSHSQPPPPQPSQVLPHDPAVAAVGPSMPFPPQSFPSHGTDYLLPSRPPLFPPHNYINQGLGFPQNPNPNPNLNPNLINPNPNWHLNFLQNHHQMNNQSLFDDLSKLGFYNNNQQQQDRQNKLVFGTLHSDDQISKVSRNSNMDYDLANIEKHLLKERELIMGNSRLNGSEIDFHRNAGLMQNIQTGTLEFGNYGSKGAPSQQQVRRIPPPGFSSNPRSAWKPNSEHNV...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_022697`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_022697

Location Chr05:5220461-5224007 (-)

Description Similar to URT1: UTP:RNA uridylyltransferase 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g45620`	UTP:RNA uridylyltransferase with a marked preference for uridine polymerization and a distributive activity for the first added nucleotides.	Uridylation prevents 3' trimming of oligoadenylated mRNAs.2013 · DOI: 10.1093/nar/gkt465 Synergistic and independent actions of multiple terminal nucleotidyl transferases in the 3' tailing of small RNAs in Arabidopsis.2015 · DOI: 10.1371/journal.pgen.1005091 Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis.2015 · DOI: 10.1371/journal.pgen.1005119 Uridylation and PABP Cooperate to Repair mRNA Deadenylated Ends in Arabidopsis.2016 · DOI: 10.1016/j.celrep.2016.02.060 A genetics screen highlights emerging roles for CPL3, RST1 and URT1 in RNA metabolism and silencing.2019 · DOI: 10.1038/s41477-019-0419-7 The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis.2021 · DOI: 10.1038/s41467-021-21382-2

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_022697 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening Biological Process

GO:0006397 mRNA processing Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0010586 miRNA metabolic process Biological Process

GO:0010587 miRNA catabolic process Biological Process

GO:0010605 negative regulation of macromolecule metabolic process Biological Process

GO:0031054 pre-miRNA processing Biological Process

GO:0031123 RNA 3'-end processing Biological Process

GO:0070935 3'-UTR-mediated mRNA stabilization Biological Process

GO:0141008 transposable element silencing by mRNA destabilization Biological Process

GO:1900369 negative regulation of post-transcriptional gene silencing by regulatory ncRNA Biological Process

GO:1990074 polyuridylation-dependent mRNA catabolic process Biological Process

KEGG gene cross-reference

ath:AT2G45620

hsa:79670

spo:2539762

spo:2543204

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Cytoplasm0.524

Rank 1 · LXL04_022697 · OH-1004

Nucleus0.371

Rank 2 · LXL04_022697 · OH-1004

Cell membrane0.148

Rank 3 · LXL04_022697 · OH-1004

Endoplasmic reticulum0.073

Rank 4 · LXL04_022697 · OH-1004

Golgi apparatus0.058

Rank 5 · LXL04_022697 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF22600.3MTPAP-like_central404-533 aa

PF19088.7TUTase415-514 aa

PF03828.25PAP_assoc622-680 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022697	`PF22600.3`	MTPAP-like_central	404	533	1.3e-31	110.3
LXL04_022697	`PF19088.7`	TUTase	415	514	9.3e-12	45.6
LXL04_022697	`PF03828.25`	PAP_assoc	622	680	3.1e-19	69.7

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`O64642`	Arabidopsis thaliana	UTP:RNA uridylyltransferase 1	50.767%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card